leonardo collado-torreslcolladotor.github.io/cv/en_cv_lcollado.pdfleonardo collado-torres, marc k....
TRANSCRIPT
2016
2011Johns Hopkins Bloomberg School of Public Health
Baltimore, MD, USA
PhD., Biostatistics
Advisors: Jeffrey T. Leek and Andrew E. JaffeThesis: Annotation-Agnostic Differential Expression and BindingAnalyses.Description: The goal was to develop statistical methods and softwarethat enable researchers to differentiate the sources of variation observedin RNA-seq while minimizing the dependance on known annotation.This allows researchers to correct for technological variation and studythe biological variation driving their phenotype of interest. We appliedthese methods to further our understanding of neuropsychiatric disor-ders using the Lieber Institute for Brain Development human brains col-lection (> 1000 samples).
2009
2005National Autonomous University of Mexico (UNAM)
Cuernavaca, Morelos, Mexico
B.S., Genomic Sciences
Grade 9.71/10Third generation at LCG-UNAM
Download a PDF of this CV
CONTACT [email protected]
fellgernon
lcolladotor
lcolladotor.github.io
lcollado
orcid
scholar
speaker-deck
slideshare
publons
LANGUAGE SKILLSR
Bash
Git/GitHub
Made with the R package page-down.
The source code is available atgithub.com/lcolladotor/cv and is
powered by nstrayer/cv.
Last updated on 2020-03-08.
LEONARDO COLLADO-TORRESAt the Lieber Institute for Brain Development, I am part of the Data Scienceteam whose goals include better understanding and characterizing genomicssignatures in the human brain. We use high-throughput technologies such asDNA methylation and RNA sequencing. I help mentor other team members,provide support for LIBD projects and I am advancing my academic career aspart of Andrew Jaffe’s lab.
As a quick background, I graduated from the Undergraduate Program on Ge-nomic Sciences from the National Autonomous University of Mexico (UNAM) in2009 and worked for two years at Winter Genomics analyzing high-throughputsequencing data. I then got a PhD in the Department of Biostatistics at JohnsHopkins Bloomberg School of Public Health thanks to a CONACyT scholarshipawarded in 2011. I worked with Jeff Leek and Andrew Jaffe in developing der�nd-er, regionReport, recount as well as other applied projects.
Every day I use R and Bioconductor. Occasionally I blog about them and othertools. I’m a co-founder of the LIBD rstats club and the CDSBMexico communityof R and Bioconductor developers in Latin America.
EDUCATION
|
• •
•
|
• •
2005
2002ITESM Campus Cuernavaca Cuernavaca, Morelos, MexicoH.S.
Grade 97.8/100Best high school average ( 200 students): awarded ITESM system 90%scholarship for college studies, declined to join LCG-UNAM.
2016
2011Johns Hopkins Bloomberg School of Public Health
Baltimore, MD, USA
Je� Leek lab
Research Assistant
2011
2009IBT-UNAM Cuernavaca, Morelos, MexicoEnrique Morett Lab
BioinformaticianIdenti�ed transcriptions start sites and transcription units in Escherichiacoli and Geobacter sulfurreducens with RNA-seq data. Developed theBacterialTranscription R package.
2009
2007CCG-UNAM Cuernavaca, Morelos, MexicoGuillermo Dávila Lab
Undergrad research assistantDetermined bacteriophage ecological groups by developing a methodbased on codon distribution of all phage sequenced genomes. Jointwork with Sur Herrera-Paredes.
2007Harvard University Boston, MA, USRoberto Kolter lab
Undergrad research assistantSupervisor: Elizabeth Shank. Carried out screenings to identify bacteriathat activate the production of exopolysaccharide through the activationof the gene tasA in Bacillus subtilis.
|
• •
RESEARCH EXPERIENCE
|
•
|
• •
|
• •
• •
Lieber Institute for Brain Development Baltimore, MD, USAAndrew Ja�e Lab
Staff Scientist IIAt LIBD, Dr. Collado-Torres is part of the Data Science team which goalsinclude better understanding and characterizing genomics signatures inthe human brain, including DNA methylation and gene expression.Leonardo helps mentor other team members, provides support for LIBDprojects and is advancing his academic career as part of Andrew Jaffe’slab. He is also a co-founder of the LIBD rstats club and CDSB.
2011
2009Winter Genomics Cuernavaca, Morelos, MexicoData Science Division Leader
Responsible for recruiting and hiring new personnel, overseeing and su-pervising bioinformaticians, training new employees, writing research re-ports and presenting them to colleagues, and organizing all scienti�cprojects.First scienti�c staff member at Winter Genomics; Projects completed: -de novo genome assembly simulations,assembly and annotation of the phiVC8 bacteriophage genome,integrated analysis of more than 20 RNA-seq samples for determinationof transcription initiation in Escherichia coli reported in Gama-Castro etal., PMID 21051347,de novo assembly of four Escherichia coli strains and lead to Aguilar etal., PMID 22884033; Designed training material for new employees.
2019
2010BioC2019, BioC2017, BioC2014, useR2013, BioC2011, From FunctionalGenomics to Systems Biology 2010 and BiocDevelEurope 2010
Travel awards
Taught a workshop on recount at BioC2017. Taught a workshop on re-count at BioC2017, Gave a talk on BacterialTranscription atBiocDevelEurope2010.BioC2019 scholarship application
2019announcementrstudio::conf 2019 diversity award recipient
Scholarship application.
2019http://researchsymbionts.orgEarly Career Clinical Research Symbiont Award
For our work on recount2.
• •
INDUSTRY EXPERIENCE
I typically like creating or joiningR clubs, advocate in favor of ver-sion control, �nd some time tokeep up with developments in R,and �gure out how we can worktogether better: from usinggoogle docs for writing papers tolearning from our search history.
|
•
•
• •
•
HONORS AND AWARDS
|
•
•
•
•
2018announcement CONACyT, MexicoNational Researcher level 1
2018unconf18 participants and applicationrOpenSci Unconf 2018
Worked on pkginspector.
2018announcementBioinformatics Peer Prize III
Competition website, and our winning entry.
2020
shiny app, R/Bioconductor package, analysis code
Transcriptome-scale spatial gene expression in the human dorsolateralprefrontal cortex
Kristen E Maynard , Leonardo Collado-Torres , Lukas M. Weber, CedricUytingco, Brianna K. Barry, Stephen R. Williams, Joseph L. Catallini II,Matthew N. Tran, Zachary Besich, Madhavi Tippani, Jennifer Chew, YifengYin, Joel E. Kleinman, Thomas M. Hyde, Nikhil Rao, Stephanie C. Hicks,Keri Martinowich , Andrew E Jaffe . bioRxiv 969931 (2020). doi:10.1101/2020.02.28.969931Co-�rst authorTwitter summary
2020
2019related code. Used data from recount2 and code fromrecount.bwtool
Recounting the FANTOM CAGE–Associated Transcriptome
Eddie-Luidy Imada , Diego Fernando Sanchez , Leonardo Collado-Torres, Christopher Wilks, Tejasvi Matam, Wikum Dinalankara, AlekseyStupnikov, Francisco Lobo-Pereira, Chi-Wai Yip, Kayoko Yasuzawa, NaotoKondo, Masayoshi Itoh, Harukazu Suzuki, Takeya Kasukawa, Chung-ChauHon, Michiel JL de Hoon, Jay W Shin, Piero Carninci, Andrew E Jaffe, Jef-frey T Leek, Alexander Favorov, Gloria R Franco, Benjamin Langmead ,Luigi Marchionni . Recounting the FANTOM Cage Associated Transcrip-tome. Genome Research (2020) doi: 10.1101/gr.254656 bioRxiv 659490(2019). doi: 10.1101/659490Supporting role: data preparation and adviceTwitter summary
•
•
PUBLICATIONS
indicates equal contribution, indicates corresponding author∗ †• ∗ ∗
† †
• •
|
• ∗ ∗
††
• •
2020
2019 Used data from recount2 and code from recount.bwtool
Regulatory sites for splicing in human basal ganglia are enriched fordisease-relevant information
Sebastian Guel� , Karishma D’Sa , Juan Botía , Jana Vandrovcova, Regi-na H. Reynolds, David Zhang, Daniah Trabzuni, Leonardo Collado-Torres,Andrew Thomason, Pedro Quijada Leyton, Sarah A. Gagliano, Mike A.Nalls, International Parkinson’s Disease Genomics Consortium (IPDGC),UK Brain Expression Consortium, Kerrin S. Small, Colin Smith, Adaikala-van Ramasamy, John Hardy, Michael E. Weale , Mina Ryten . Regulatorysites for known and novel splicing in human basal ganglia are enrichedfor disease-relevant information. Nature Communications (2020) doi:10.1038/s41467-020-14483-x. bioRxiv 591156 (2019). doi: 10.1101/591156Supporting role: data preparation and adviceTwitter summary
2020
2018Web browser
Dissecting transcriptomic signatures of neuronal di�erentiation andmaturation using iPSCs
Emily E Burke , Joshua G Chenoweth , Joo Heon Shin, Leonardo Colla-do-Torres, Suel Kee Kim, Nicola Micali, Yanhong Wang, Carlo Colantuoni,Richard E Straub, Daniel J Hoeppner, Huei-Ying Chen, Alana Sellers,Kamel Shibbani, Gregory R Hamersky, Marcelo Diaz Bustamante, BaDoiN Phan, William S Ulrich, Cristian Valencia, Amritha Jaishankar, AmandaJ Price, Anandita Rajpurohit, Stephen A Semick, Roland Bürli, James CBarrow, Daniel J Hiler, Stephanie C Page, Keri Martinowich, Thomas MHyde, Joel E Kleinman, Karen F Berman, José A Apud, Alan J Cross, Nick JBrandon, Daniel R Weinberger, Brady J Maher, Ronald DG McKay , An-drew E Jaffe . Dissecting transcriptomic signatures of neuronal differen-tiation and maturation using iPSCs. Nature Communications (2020) doi:10.1038/s41467-019-14266-z bioRxiv 380758 (2018). doi: 10.1101/380758Supporting role: analysisTwitter summary
2019 Characterizing the dynamic and functional DNA methylation landscapein the developing human cortex
Kira A Perzel Mandell , Amanda J Price, Richard Wilton, Leonardo Colla-do-Torres, Ran Tao, Nicholas J Eagles, Alexander S Szalay, Thomas MHyde, Daniel R Weinberger, Joel E Kleinman, Andrew E Jaffe . Character-izing the dynamic and functional DNA methylation landscape in the de-veloping human cortex. bioRxiv 823781 (2019). doi: 10.1101/823781Supporting role: analysisTwitter summary
2019
shiny app, code
recount-brain: a curated repository of human brain RNA-seq datasetsmetadata
Ashkaun Razmara, Shannon E Ellis, Dustin J Sokolowski, Sean Davis,Michael D Wilson, Jeffrey T Leek, Andrew E Jaffe, Leonardo Collado-Tor-res . recount-brain: a curated repository of human brain RNA-seqdatasets metadata. bioRxiv 618025 (2019). doi: 10.1101/618025Corresponding authorTwitter summary
|
• ∗ ∗ ∗
† †
• •
|
• ∗ ∗
††
• •
• ∗
†
• •
•
†
• •
2019
2018
shiny web application
Divergent neuronal DNA methylation patterns across human corticaldevelopment reveal critical periods and a unique role of CpHmethylation.
Amanda J. Price , Leonardo Collado-Torres , Nikolay A. Ivanov, Wei Xia,Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M.Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E Jaffe . Divergentneuronal DNA methylation patterns across human cortical developmentreveal critical periods and a unique role of CpH methylation. Genome Bi-ology 2019. doi: 10.1186/s13059-019-1805-1. bioRxiv 428391 (2018). doi:10.1101/428391Co-�rst authorTwitter summary and summary numbertwo
2019
2018
web browser
Regional heterogeneity in gene expression, regulation, and coherence inthe frontal cortex and hippocampus across development andschizophrenia
Leonardo Collado-Torres, Emily E Burke, Amy Peterson, JooHeon Shin,Richard E Straub, Anandita Rajpurohit, Stephen A Semick, William S Ul-rich, BrainSeq Consortium, Amanda J Price, Cristian Valencia, Ran Tao,Amy Deep-Soboslay, Thomas M Hyde, Joel E Kleinman, Daniel R Wein-berger , Andrew E Jaffe . Regional heterogeneity in gene expression,regulation, and coherence in the frontal cortex and hippocampus acrossdevelopment and schizophrenia. Neuron 2019. doi:10.1016/j.neuron.2019.05.013 bioRxiv 426213 (2018). doi: 10.1101/426213First-authorTwitter summary
2019
2018
Comprehensive assessment of multiple biases in small RNA sequencingreveals signi�cant di�erences in the performance of widely usedmethods.
Carrie Wright , Anandita Rajpurohit , Emily E. Burke, Courtney Williams,Leonardo Collado-Torres, Martha Kimos, Nicholas J. Brandon, Alan J.Cross, Andrew E. Jaffe, Daniel R. Weinberger , Joo Heon Shin .Compre-hensive assessment of multiple biases in small RNA sequencing revealssigni�cant differences in the performance of widely used methods. BMCGenomics (2019). doi: 10.1186/s12864-019-5870-3. bioRxiv 445437 (2018).doi: 10.1101/445437Supporting roleTwitter summary
|
• ∗ ∗
†
• •
|
•
† †
• •
|
• ∗ ∗
† †
• •
2019
Used data from recount2.
Integrated Transcriptomic and Proteomic Analysis of Primary HumanUmbilical Vein Endothelial Cells.
Anil K Madugundu, Chan Hyun Na, Raja Sekhar Nirujogi, SantoshRenuse, Kwang Pyo Kim, Kathleen H. Burns, Christopher Wilks, BenLangmead, Shannon E. Ellis, Leonardo Collado-Torres, Marc K. Halushka,Min-Sik Kim, Akhilesh Pandey . Integrated Transcriptomic and Proteom-ic Analysis of Primary Human Umbilical Vein Endothelial Cells. Pro-teomics 2019. doi: 10.1002/pmic.201800315Supporting roleTwitter summary
2019
2018
Integrated DNA methylation and gene expression pro�ling across multi-ple brain regions implicate novel genes in Alzheimer’s disease.
Stephen A Semick, Rahul A Bharadwaj, Leonardo Collado-Torres, RanTao, Joo Heon Shin, Amy Deep-Soboslay, James R. Weiss, Daniel R Wein-berger, Thomas M Hyde, Joel E Kleinman, Andrew E Jaffe , Venkata SMattay . Integrated DNA methylation and gene expression pro�lingacross multiple brain regions implicate novel genes in Alzheimer’s dis-ease. Acta Neuropathologica 2019. doi: 10.1007/s00401-019-01966-5. bioRx-iv 430603 (2018). doi: 10.1101/430603Supporting role: analysisTwitter summary
2018
Used data from recount2 and code from recount.bwtool
Incomplete annotation of OMIM genes is likely to be limiting the diag-nostic yield of genetic testing, particularly for neurogenetic disorders.
David Zhang , Sebastian Guel� , Sonia Garcia Ruiz, Beatrice Costa, Regi-na H Reynolds, Karishma D’Sa, Wenfei Liu, Thomas Courtin, Amy Peter-son, Andrew E Jaffe, John Hardy, Juan Botia, Leonardo Collado-Torres,Mina Ryten. Incomplete annotation of OMIM genes is likely to be limitingthe diagnostic yield of genetic testing, particularly for neurogenetic dis-orders. bioRxiv 499103 (2018). doi: 10.1101/499103Supervisor role, data generation, overall project adviceTwitter summary
2018
Data available from recount2.
RNA-seq transcript quanti�cation from reduced-representation data inrecount2
Fu J, Kammers K, Nellore A, Collado-Torres L, Leek JT, Taub MA. RNA-seqtranscript quanti�cation from reduced-representation data in recount2.bioRxiv 247346 (2018). doi: 10.1101/247346Supporting roleTwitter summary
•
†
• •
|
•
††
• •
• ∗ ∗
• •
•
• •
2018 Non-coding Class Switch Recombination-Related Transcription in Hu-man Normal and Pathological Immune Responses.
Helena Kuri-Magaña, Leonardo Collado-Torres, Andrew E Jaffe, Humber-to Valdovinos-Torres, Marbella Ovilla-Muñoz, Juan M Téllez-Sosa, Laura CBonifaz-Alfonzo, Jesús Martínez-Barnetche. Non-coding Class Switch Re-combination-Related Transcription in Human Normal and PathologicalImmune Responses. Frontiers in Immunology 2018. doi:10.3389/�mmu.2018.02679 bioRxiv 384172 (2018). doi: 10.1101/384172Supporting role: data preparation and adviceTwitter summary
2018
2017
Developmental e�ects of maternal smoking during pregnancy on thehuman frontal cortex transcriptome.
Semick SA, Collado-Torres L, Markunas CA, Shin JH, Deep-Soboslay A,Tao R, Huestis MA, Bierut LJ, Maher BS, Johnson EO, Hyde TM, Weinberg-er DR, Hancock DB, Kleinman JE , Jaffe AE . Developmental effects ofmaternal smoking during pregnancy on the human frontal cortex tran-scriptome. Molecular Psychiatry 2018. doi: 110.1038/s41380-018-0223-1. bio-Rxiv 236968 (2017). doi: 10.1101/236968Supporting role: analysisTwitter summary
2018
2017
Developmental and genetic regulation of the human cortex transcrip-tome illuminate schizophrenia pathogenesis.
Jaffe AE, Straub R, Shin JH, Tao R, Gao Y, Collado-Torres L, Kam-Thong T,Xi HS, Quan J, Chen Q, Colantuoni C, Ulrich WS, Maher BJ, Deep-SoboslayA, The BrainSeq Consortium, Cross AJ, Brandon NJ, Leek JT, Hyde TM,Kleinman JE, Weinberger DR. Developmental and genetic regulation ofthe human cortex transcriptome illuminate schizophrenia pathogenesis.Nat. Neurosci. 2018. doi: 10.1038/s41593-018-0197-y. bioRxiv 124321 (2017).doi: 10.1101/145656Supporting role: analysisTwitter summary
2018
2017
Improving the value of public RNA-seq expression data by phenotypeprediction.
Ellis SE, Collado-Torres L, Jaffe AE, Leek JT. Improving the value of publicRNA-seq expression data by phenotype prediction. Nucl. Acids Res. 2018.doi: 10.1093/nar/gky102 bioRxiv 145656 (2017). doi: 10.1101/145656Supporting role: data preparation and adviceTwitter summary and this tweet
•
• •
|
•
† †
• •
|
•
• •
|
•
• •
2017 Accessing over 70,000 human RNA-seq samples with Bioconductor
Collado-Torres L , Nellore A, Jaffe AE. recount work�ow: Accessing over70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1approved, 2 approved with reservations]. F1000Research (2017). doi:10.12688/f1000research.12223.1. Winning entry for the Bioinformatics PeerPrize III.First and corresponding authorTwitter summary
2017 Altered expression of histamine signaling genes in autism spectrumdisorder
Wright C, Shin JH, Rajpurohit A, Deep-Soboslay A, Collado-Torres L, Bran-don NJ, Hyde TM, Kleinman JE, Jaffe AE, Cross AJ, Weinberger DR. Al-tered expression of histamine signaling genes in autism spectrum disor-der. Translational Psychiatry 2017. doi: 10.1038/tp.2017.87Supporting role: visualizationTwitter summary
2017
2016
Reproducible RNA-seq analysis using recount2
Collado-Torres L , Nellore A , Kammers K, Ellis SE, Taub MA, Hansen KD,Jaffe AE, Langmead B, Leek JT. Reproducible RNA-seq analysis using re-count2 Nature Biotechnology 2017. doi: 10.1038/nbt.3838 bioRxiv 068478(2016). doi: 10.1101/068478Co-�rst authorTwitter summary
2016 Human splicing diversity and the extent of unannotated splice junctionsacross human RNA-seq samples on the Sequence Read Archive.
Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L,Wang S, Phillips RA, Karbhari N, Hansen KD, Langmead B, Leek JT. Hu-man splicing diversity and the extent of unannotated splice junctionsacross human RNA-seq samples on the Sequence Read Archive.Genome Biology 2016. doi: 10.1186/s13059-016-1118-6. bioRxiv 038224(2016). doi: 10.1101/038224Supporting role: analysisbioRxiv tweet
2016 Flexible expressed region analysis for RNA-seq with der�nder.
Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B,Irizarry RA, Leek JT, Jaffe AE. Flexible expressed region analysis for RNA-seq with der�nder. Nucl. Acids Res. 2016. doi: 10.1093/nar/gkw852 bioRxiv015370 (2016). doi: 10.1101/015370First authorTwitter summary
• †
• •
•
• •
|
• ∗ ∗
• •
•
• •
•
• •
2016
2015
Rail-RNA: Scalable analysis of RNA-seq splicing and coverage.
Nellore A, Collado-Torres L, Jaffe AE, Alquicira-Hernández J, Wilks C, PrittJ, Morton J, Leek JT, Langmead B. Rail-RNA: Scalable analysis of RNA-seqsplicing and coverage. Bioinformatics 2016. doi:10.1093/bioinformatics/btw575 bioRxiv 019067 (2015). doi: 10.1101/019067Supporting role: analysisTwitter summary
2016
2015
regionReport: Interactive reports for region-level and feature-level ge-nomic analyses
Collado-Torres L, Jaffe AE and Leek JT. regionReport: Interactive reportsfor region-level and feature-level genomic analyses [version2; referees: 2approved, 1 approved with reservations]. F1000Research 2016, 4:105. doi:10.12688/f1000research.6379.2 bioRxiv 016659 (2015). doi: 10.1101/016659First authorTwitter summary
2015 Developmental regulation of human cortex transcription and its clinicalrelevance at single base resolution.
Jaffe AE, Shin J, Collado-Torres L, Leek JT, et al. Developmental regulationof human cortex transcription and its clinical relevance at single baseresolution. Nat. Neurosci. 2015. doi: 10.1038/nn.3898Supporting role: analysisTwitter summary
2014 Book chapter: Measurement, Summary, and Methodological Variation inRNA-sequencing
Frazee AC, Collado-Torres L, Jaffe AE, Langmead B, Leek JT. Measure-ment, Summary, and Methodological Variation in RNA-sequencing inStatistical Analysis of Next Generation Sequencing Data, Springer, 2014,115-128.
2011 Interspecies interactions that result in Bacillus subtilis forming bio�lmsare mediated mainly by members of its own genus.
Shank EA, Klepac-Ceraj V, Collado-Torres L, Powers GE, Losick R, Kolter R.Interspecies interactions that result in Bacillus subtilis forming bio�lmsare mediated mainly by members of its own genus. Proc. Natl. Acad. Sci.U.S.A. 2011 Nov;108(48):E1236–1243. doi: 10.1073/pnas.1103630108Supporting role: performed initial experimentsTwitter summary from 2011? No such thing back then
|
•
• •
|
•
• •
•
• •
•
•
• •
2011 RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).
Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muñiz-Ras-cado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, García-Sotelo JS,López-Fuentes A, Porrón-Sotelo L, Alquicira-Hernández S, Medina-RiveraA, Martínez-Flores I, Alquicira-Hernández K, Martínez-Adame R, Bona-vides-Martínez C, Miranda-Ríos J, Huerta AM, Mendoza-Vargas A, Colla-do-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R,Morett E, Collado-Vides J. RegulonDB version 7.0: transcriptional regula-tion of Escherichia coli K-12 integrated within genetic sensory responseunits (Gensor Units). Nucleic Acids Res. 2011 Jan;39(Database issue):D98–105. doi: 10.1093/nar/gkq1110
2014
2020spatialLIBD: LIBD Visium spatial transcriptomics human pilot datainspector – (Not Available on 2020-03-08) downloads. GenomicState:data for der�nder analyses – (Not Available on 2020-03-08) down-loads. recount: Explore and download data from the recount project– 20884 downloads. der�nder: Annotation-agnostic differential ex-pression analysis of RNA-seq data at base-pair resolution via the DERFinder approach – 29794 downloads. der�nderPlot: plotting func-tions for der�nder results – 12440 downloads. regionReport: Gener-ate HTML or PDF reports for a set of genomic regions orDESeq2/edgeR results – 14409 downloads. der�nderHelper: helperfunctions for der�nder package – 24458 downloads. der�nderData:data for der�nder examples – 2868 downloads.
Bioconductor: author role
2020regutools RemotelyMentor role
Mentored three CDSB alumni while they developed their �rst R/Biocon-ductor package.
2019
2014brain�owprobes, bumphunter, ballgownBioconductor: contributor role
2019
2011sgejobs: Helper functions for SGE jobs at JHPCE. easyweb: A fast andeasy way to build your own website. libdRSE: Custom RSE objectsfrom genomic coordinates on LIBD data. blogdown: contributed theInsert Image and New Post addins. recount.bwtool: Compute cover-age matrices from recount quickly using bwtool. jaffelab: commonlyused functions by the Jaffe lab. shinycsv: explore a table interactively.enrichedRanges: identify enrichment between two sets of genomicranges. dots: simplify function calls. �tbitR: visualize your FitBit data.BacterialTranscription: identify TSSs and TUs from RNA-seq data.
Misc R packages
•
SOFTWARE
all_purpose: R, Ranked220/8606 (top 2.5%) in the USand 799/72425 (top 1%) world-wide by GitHub Awards as ofMarch 1st, 2020. Does not takeinto account contributions atGitHub organizations.statistics: Statascripting: bashmarkup: LaTeX, markdownOS: Linuxcluster queue: Son of GridEngine
|
•
|
|
2019
2014recount-brain: explore recount-brain interactively. wgbsExprs: LIBDWGBS Expression explorer for the methylation and expression asso-ciations described by Price et al, 2019. shinycsv: explore a table inter-actively. recount:: analysis-ready RNA-seq gene and exon countsdatasets. MPH capstone TA of�ce hours sign up. Simple mortgagecalculator.
shiny web applications
Deployed links: recount-brain, wgbsExprs, recount, shinycsv.
2016GitHub and OverleafJHU thesis template
2020
2011Develop and maintain open-source biostatistical softwareOpen-source software
2020
2013Biostatistics, Bioinformatics, F1000Research, Nucleic Acids Research,Scienti�c Reports, Statistical Applications in Genetics and MolecularBiology.
Peer Review
Full details available through Publons.
2020
2018Co-founder and Board Member of CDSB which is a community of Rand Bioconductor developers in Latin America.
Community of Bioinformatics Software Developers (CDSB in Spanish)
2020
2018Co-founder and Maintainer of the LIBD rstats club.
Baltimore, MD, USA
LIBD rstats club
2016
Student representative for the Centennial celebration of the Depart-ment of Biostatistics.
Baltimore, MD, USA
JHBSPH Student rep
2016
2012Organized Cultural Mixer events for the Department of Biostatisticswith Amanda Mejia for raising cultural awareness.
Baltimore, MD, USA
JHBSPH Biostatistics Cultural Mixers
2014International Society for Computational Biology (2019), American So-ciety of Human Genetics (2015, 2018-2019), American Statistical Asso-ciation (2015-2017, 2020), ENAR student member (2014-2016), Ameri-can Public Health Association (2014).
Professional memberships
2014
2012Organized the Genomics for Students group (website).
Baltimore, MD, USA
JHBSPH Genomics for students
2011
2009Organized a Genomics Journal Club at IBT-UNAM.
Cuernavaca, Morelos, Mexico
IBT-UNAM Genomics Journal Club
|
•
LEADERSHIP AND SERVICE
|
|
•
|
|
|
|
|
2009
2008Elected class representative for the LCG Academic Committee. Classrepresentative for Administration Unit for Technology Informationcommittee.
Cuernavaca, Morelos, Mexico
LCG-UNAM Student rep
2008Helped start the National Node of Bioinformatics (Mexico) online fo-rum.
Cuernavaca, Morelos, Mexico
NNB-UNAM forum launch
2020
2019Along with Alejandro Reyes, co-mentored Joselyn Chávez, CarminaBarberena-Jonas and Jesus Emiliano Sotelo-Fonseca for the CDSBregutools R/Bioconductor package project.
Remotely
CDSB regutools project
2018
2017MPH practicum and MPH capstone advisor. Baltimore, MD, USAAmy Peterson
2018
2017MPH practicum and MPH capstone advisor. Baltimore, MD, USAAshkaun Razmara
2015
LCG-UNAM student visiting Jeff Leek’s group. Baltimore, MD, USAJosé Alquicira-Hernández
2011
2009Advised and trained 13 LCG-UNAM students and alumni while work-ing at Winter Genomics: Riveros-McKay F, Vargas-Chávez C, Dulanto-Acevedo V, Romero-Martínez S, Samaniego-Castruita J, Zepeda-Men-doza L, Vargas-Velázquez A, Noé-González M, Soto Jiménez LM,López Moyado I, Medina-Abarca H., Izquierdo-Rangel E, and Berrocal-Quezada NA.
Cuernavaca, Morelos, Mexico
Winter Genomics mentees
|
MENTORING EXPERIENCE
|
|
|
|
2009Trained 3 LCG-UNAM students to take over the R/Bioconductorcourse: Reyes-Quiroz A, Moreno-Mayar V, and Reyes-López J.
Cuernavaca, Morelos, Mexico
LCG-UNAM mentees
2019CDSB at LCG-UNAM Cuernavaca, Morelos, MexicoCDSB
Organizer and instructor for the CDSB 2019 workshop.
2016Johns Hopkins University Dubai, UAEKandahar University Training
Instructor for a Biostatistics and Stata workshop for Kandahar UniversityFaculty, organized by Johns Hopkins University (website).
2016INMEGEN Mexico City, CDMX, MexicoGenomeeting
Instructor for Genomeeting 2016.
2016
2014Johns Hopkins Bloomberg School of Public Health
Baltimore, MD, USA
Statistical Methods in Public Health
Lead teaching assitant for Statistical Methods in Public Health I and II.
2016
2014Johns Hopkins Bloomberg School of Public Health
Baltimore, MD, USA
MPH capstone project
Teaching assitant for the MPH capstone projects. 30 min one-on-oneconsulting sessions (biostatistics, Stata coding).Develop and maintain the MPHcapstoneTA shiny application.
TEACHING EXPERIENCE
I am a strong believer that ac-cess to education is important,but also having mentors andsponsors and as such as I aim tobe a good mentor and help oth-ers by promoting them amongmy peers and helping them be-come more visible in the re-search community. My most di-rect way of helping is throughthe Community of Bioinformat-ics Software Developers thataims to help R/Bioconductorusers become R/Bioconductordevelopers. I also strongly be-lieve in giving back to your owncommunity by passing on theknowledge you acquired at acourse or conference. Historical-ly, that’s what launched my ca-reer in R and I learn a lot fromteaching.
•
•
•
|
•
|
•
•
2016
2012Johns Hopkins Bloomberg School of Public Health
Baltimore, MD, USA
Statistical Methods in Public Health
Teaching assitant for Statistical Methods in Public Health I, II, III and IV.
2015Johns Hopkins Bloomberg School of Public Health
Baltimore, MD, USA
Summer Institute
Guest lecturer: Introduction to R for Public Health Researchers, Repro-ducible research module.
2015Johns Hopkins Bloomberg School of Public Health
Baltimore, MD, USA
Introduction to R for Public Health Researchers
Teaching assistant
2012
2011LCG-UNAM Cuernavaca, Morelos, MexicoIntroduction to R and Biostatistics
Guest lecturer: Seminar 1, Introduction to Bioinformatics course
2011CCG-UNAM Cuernavaca, Morelos, MexicoPDCB-UNAM
Instructor for the course Introduction to R and Biostatistics for Bio-medical Sciences Ph.D. students (website).
2010CCG-UNAM Cuernavaca, Morelos, MexicoPDCB-UNAM
Instructor for Analysis of High-Throughput Sequencing data with Bio-conductor for Biomedical Sciences Ph.D. students (website).
2010Organized by NNB-UNAM at CCG-UNAM
Cuernavaca, Morelos, Mexico
National Bioinformatics Week
Instructor of the Introduction to Using Bioconductor for High-Through-put Sequencing Analysis practice lab at the National BioinformaticsWeek.
2010IBT-UNAM Cuernavaca, Morelos, MexicoEnrique Morett Lab
Instructor for the Introduction to R and plotting with R course forMorett’s lab.
2010IBT-UNAM Cuernavaca, Morelos, MexicoStatistical Methods and Analysis of Genomic Data
Organizer and instructor (website).
|
•
•
•
|
•
•
•
•
•
•
2009IBT-UNAM Cuernavaca, Morelos, MexicoEnrique Morett Lab
Organizer and instructor for the course Introduction to Bioinformaticsfor Morett’s lab where I taught the Introduction to R and plotting with Rmodule (website)
2009LCG-UNAM Cuernavaca, Morelos, MexicoSeminar III: R/Bioconductor
Organizer and instructor for an in-depth Bioconductor course (website)
2009LCG-UNAM Cuernavaca, Morelos, MexicoPrinciples of Statistics
Basic R (website).
2008LCG-UNAM Cuernavaca, Morelos, MexicoBioinformatics and Statistics I
R and Bioconductor overview (website).
2020 San Francisco, CA, USA
rstudio::conf
Attended the JavaScript for Shiny users workshop taught by GarrickAden-Buie.
2019 Houston, TX, USA
ASHG
Platform talk: Regional heterogeneity in gene expression, regulation,and coherence in the frontal cortex and hippocampus across develop-ment and schizophrenia (slides).
2019LIIGH-UNAM Juriquilla, Qro, MexicoVisitors Research Seminar
Analyzing BrainSeq Phase II and generating the recount-brain resource(slides).
2019LCG-UNAM Cuernavaca, Morelos, MexicoCDSB launch keynote
Launch of the CDSB 2019 workshop (slides).
•
•
•
•
COURSES, MEETINGS, TALKS, AND POSTERS
Most recent slides are availablevia speakerdeck or slideshare.
•
•
•
•
2019Rockefeller University New York, NY, USABioC
Using the recount2 resource and related tools workshop (slides). Light-ning talk on the Community of Bioinformatics Software Developers(slides).Also remotely for CONABIO’s bioinformatics course on 2019-10-07 orga-nized by Alicia Mastretta-Yanes.
2019Cold Spring Harbor Laboratory Cold Spring Harbor, NY, USABiology of Genomes (BoG)
recount-brain: a curated repository of human brain RNA-seq datasetsmetadata (poster).
2019
LIBD Baltimore, MD, USASta� Seminar Series
Analyzing BrainSeq Phase II and generating the recount-brain resource(slides).
2019 Austin, TX, USA
rstudio::conf
Attended the Building Tidy Tools workshop by Charlotte and HadleyWickham.
2019 Hawaii, HI, USA
Paci�c Symposium on Biocomputing (PSB)
Reproducible RNA-seq analysis with recount2 (slides). Regional hetero-geneity in gene expression, regulation and coherence in hippocampusand dorsolateral prefrontal cortex across development and in schizo-phrenia (poster).
2018Johns Hopkins University Baltimore, MD, USAJoint Genomic Meeting
recount-brain: a curated repository of human brain RNA-seq datasetsmetadata (slides).
2018Cold Spring Harbor Laboratory Cold Spring Harbor, NY, USABiological Data Science
Regional heterogeneity in gene expression, regulation and coherence inhippocampus and dorsolateral prefrontal cortex across developmentand in schizophrenia (poster).
2018 San Diego, CA, USA
ASHG
Regional heterogeneity in gene expression, regulation and coherence inhippocampus and dorsolateral prefrontal cortex across developmentand in schizophrenia (poster).
•
•
•
•
•
•
•
•
•
2018Keynote RemotelyCDSB
From learning to using to teaching to developing R (remote presenta-tion) (slides).
2018 Philadelphia, PA, USA
SAGES
BrainSeq Phase II: schizophrenia-associated expression differences be-tween the hippocampus and the dorsolateral prefrontal cortex (poster).
2018
LCG-UNAM RemotelyLCG-UNAM Remote Talks
Reproducible RNA-seq analysis with recount2 and recount-brain (slides).
2018 New York, NY, USA
SOBP
Unique Molecular Correlates of Schizophrenia and Its Genetic Risk in theHippocampus Compared to Frontal Cortex (slides).
2018Cold Spring Harbor Laboratory Cold Spring Harbor, NY, USABiology of Genomes (BoG)
BrainSeq Phase II: Schizophrenia-associated expression differences be-tween the hippocampus and the dorsolateral prefrontal cortex (slides).
2018 Seattle, WA, USA
rOpenSci Unconf
Worked on pkginspector.
2018 Remotely
Journal Club by Dennis Lal
recount work�ow: Accessing over 70,000 human RNA-seq samples withBioconductor (slides).
2017Johns Hopkins University Baltimore, MD, USAIDIES
Getting started with recount2 and accessing it via R (poster).
2017 Baltimore, MD, USA
JSM
Guiding principles for interactive graphics based on LIBD data scienceprojects (slides).
2017Johns Hopkins University Baltimore, MD, USASummer Institute
Reproducible Research and Bioinformatics (slides).
•
•
•
•
•
•
•
•
•
•
2017Dana-Farber Cancer Institute Boston, MA, USABioC
Reproducible RNA-seq analysis with recount2 workshop (slides).
2017 Chicago, IL, USA
ICSA
Reproducible RNA-seq analysis with recount2 (slides).
2017 San Diego, CA, USA
SOBP
RNA-seq samples beyond the known transcriptome with der�nder andrecount (slides).
2016Johns Hopkins University Dubai, UAEKandahar University Training
Introduction at Kandahar University MPH training event (slides).
2016INMEGEN Mexico City, CDMX, MexicoGenomeeting
recount: facilitando el análisis de miles de muestras de RNA-seq (slides).
2016 Long Beach, CA, USA
SACNAS
Using Data Science to Study Human Brain Genomic Measurements(slides).
2016 Austin, TX, USA
ENAR
Annotation-agnostic differential expression analysis (slides).
2015Johns Hopkins University Baltimore, MD, USAJoint Genomic Meeting
dbFinder (slides).
2015
Johns Hopkins University Baltimore, MD, USAIDIES
Annotation-agnostic RNA-seq differential expression analysis software(poster).
2015Johns Hopkins University Baltimore, MD, USAGenomics and Bioinformatics Symposium
Annotation-agnostic differential expression analysis (slides).
2015 Baltimore, MD, USA
ASHG
Annotation-agnostic RNA-seq differential expression analysis software(poster).
•
•
•
•
•
•
•
•
•
•
•
2015Johns Hopkins University Baltimore, MD, USABiostatistics Computing Club
Easy parallel computing with BiocParallel and HTML reports with knitr-Bootstrap (slides).
2015 Miami, FL, USA
ENAR
Dissecting human brain development at high resolution using RNA-seq(slides).
2015
Johns Hopkins University Baltimore, MD, USAJoint Genomic Meeting
Does mapping simulated RNA-seq reads provide information? (slides).
2014Johns Hopkins University Baltimore, MD, USAJe� Leek lab
der�nder tutorial (slides).
2014
INMEGEN Mexico City, CDMX, Mexicois3b: International Summer Symposium on Systems Biology
Developmental regulation of human cortex transcription at base-pairresolution (slides).
2014Dana-Farber Cancer Institute Boston, MA, USABioC
2014Johns Hopkins University Baltimore, MD, USABiostatistics Computing Club
Git for research (slides).
2014Johns Hopkins University Baltimore, MD, USAIDIES
2014 Baltimore, MD, USA
ENAR
Fast annotation-agnostic differential expression analysis (poster).
2014Johns Hopkins University Baltimore, MD, USADelta Omega Poster Competition
Fast annotation-agnostic differential expression analysis (poster).
2014 Cuernavaca, Morelos, Mexico
LCG-UNAM 10 year anniversary
Fast differential expression analysis annotation-agnostic across groupswith biological replicates (slides).
•
•
•
•
•
•
•
•
•
2013Johns Hopkins University Baltimore, MD, USAGenomics and Bioinformatics Symposium
Fast annotation-agnostic differential expression analysis (poster).
2013Johns Hopkins University Baltimore, MD, USAGenomics for Students
Introduction to ggbio (slides).
2013Johns Hopkins University Baltimore, MD, USAJoint Genomic Meeting
Fast differential expression analysis annotation-agnostic across groupswith biological replicates (slides).
2013Johns Hopkins University Baltimore, MD, USABiostatistics Journal Club
Fast differential expression analysis annotation-agnostic across groupswith biological replicates (slides).
2013 Albacete, Spain
useR!
Differential expression analysis of RNA-seq data at base-pair resolution inmultiple biological replicates (slides).
2013Johns Hopkins University Philadelphia, PA, USABiostatistics Department Retreat
Differential expression RNA-seq analysis with a large data set from brainsamples (poster).
2013
Johns Hopkins University Baltimore, MD, USABiostatistics Computing Club
Introduction to knitr (slides).
2013Johns Hopkins University Baltimore, MD, USAGenomics for Students
Introduction to High-Throughput Sequencing and RNA-seq (slides).
2012Johns Hopkins University Baltimore, MD, USAGenomics for Students
DEXSeq paper discussion (slides).
2012LCG-UNAM RemotelyLCG-UNAM Remote Talks
Introduction to R and Biostatistics (slides).
2012Johns Hopkins University Baltimore, MD, USABiostatistics Computing Club
Introducing Git while making your academic webpage (slides).
•
•
•
•
•
•
•
•
•
•
•
2011LCG-UNAM RemotelyLCG-UNAM Remote Talks
Introducing Biostatistics to �rst year LCG students (slides).
2011Fred Hutchinson Cancer Research Center Seattle, WA, USABioC
2010EMBL Heidelberg, GermanyBioconductor Developer Meeting
BacterialTranscription: a R package to identify Transcription Start Sitesand Transcription Units (slides).
2010
EMBL Heidelberg, GermanyFrom Functional Genomics to System Biology
Global Analysis of Transcription Start Sites and Transcription Units inBacterial Genomes (poster).
2010Organized by NNB-UNAM at CCG-UNAM
Cuernavaca, Morelos, Mexico
National Bioinformatics Week
Introduction to using Bioconductor for High Throughput SequencingAnalysis instructor (slides).
2010
Fred Hutchinson Cancer Research Center Seattle, WA, USABioC
Global Analysis of Transcription Start Sites and Transcription Units inBacterial Genomes (poster).
2009CCG-UNAM Cuernavaca, Morelos, MexicoLCG-UNAM Third Generation Symposium
Bacteriophages: analyzing their diversity (slides).
2009
Fred Hutchinson Cancer Research Center Seattle, WA, USABioC
2009CCG-UNAM Cuernavaca, Morelos, MexicoCourse on Oral Communication
Taught by the master Rafael Popoca.
2008Fred Hutchinson Cancer Research Center Seattle, WA, USABioC
2008LCG-UNAM Cuernavaca, Morelos, MexicoA Short R/Bioconductor Course
Taught by James Bullard from UC Berkeley, Ph.D. student in SandrineDudoit’s lab at the time.
2007 Boston, MA, USA
Boston Bacterial Meeting
•
•
•
•
•
•
•
•
2007Harvard University Boston, MA, USADepartment of Microbiology and Molecular Genetics Retreat
2006CCG-UNAM Cuernavaca, Morelos, MexicoWinter School in Genomics
2005 Kyoto, Japan
HUGO
Native: SpanishBilingual: EnglishBasic: French
LANGUAGES
• • •